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Nanoscale secondary ion mass spectrometry (nanoSIMS) and fluorescence in situ hybridization (FISH) microscopy provide high-resolution, multimodal image representations of the identity and cell activity respectively of targeted microbial…
Image partitioning, or segmentation without semantics, is the task of decomposing an image into distinct segments, or equivalently to detect closed contours. Most prior work either requires seeds, one per segment; or a threshold; or…
In medical imaging, chromosome straightening plays a significant role in the pathological study of chromosomes and in the development of cytogenetic maps. Whereas different approaches exist for the straightening task, typically geometric…
Structured illumination microscopy (SIM) has attained high spatiotemporal delineation of subcellular architecture, yet offers limited insight into chemical composition. We develop Chem-SIM, a structured-illumination fluorescence detected…
We present a method for automatic cell classification in tissue samples using an automated training set from multiplexed immunofluorescence images. The method utilizes multiple markers stained in situ on a single tissue section on a robust…
Cryo-electron microscopy (cryo-EM) is a technique for reconstructing the 3-dimensional (3D) structure of biomolecules (especially large protein complexes and molecular assemblies). As the resolution increases to the near-atomic scale,…
Understanding genetic variation, e.g., through mutations, in organisms is crucial to unravel their effects on the environment and human health. A fundamental characterization can be obtained by solving the haplotype assembly problem, which…
Phase microscopy is an invaluable tool in the biosciences and in clinical diagnostics. The sensitivity of current phase microscopy techniques is optimized for one specific mean phase value and varies significantly across a given sample.…
Multiplex immunofluorescence and immunohistochemistry benefit patients by allowing cancer pathologists to identify several proteins expressed on the surface of cells, enabling cell classification, better understanding of the tumour…
Involved in mitotic condensation, interaction of transcriptional regulatory elements or isolation of structural domains, understanding loop formation is becoming a paradigm in the deciphering of chromatin architecture and its functional…
The rapid and accurate detection of biochemical compositions in fish is a crucial real-world task that facilitates optimal utilization and extraction of high-value products in the seafood industry. Raman spectroscopy provides a promising…
The expanding adoption of digital pathology has enabled the curation of large repositories of histology whole slide images (WSIs), which contain a wealth of information. Similar pathology image search offers the opportunity to comb through…
Histopathology image analysis plays a critical role in cancer diagnosis and treatment. To automatically segment the cancerous regions, fully supervised segmentation algorithms require labor-intensive and time-consuming labeling at the pixel…
Multi-echo Chemical Shift Encoded methods for Fat-Water quantification are growing in clinical use due to their ability to estimate and correct some confounding effects. State of the art CSE water-fat separation approaches rely on a…
Histo-pathological diagnostics are an inherent part of the everyday work but are particularly laborious and associated with time-consuming manual analysis of image data. In order to cope with the increasing diagnostic case numbers due to…
Morphological atlases are an important tool in organismal studies, and modern high-throughput Computed Tomography (CT) facilities can produce hundreds of full-body high-resolution volumetric images of organisms. However, creating an atlas…
Many medical and biological protocols for analyzing individual biological cells involve morphological evaluation based on cell staining, designed to enhance imaging contrast and enable clinicians and biologists to differentiate between…
This paper presents an algorithm which aims to assist the radiologist in identifying breast cancer at its earlier stages. It combines several image processing techniques like image negative, thresholding and segmentation techniques for…
The segmentation, seen as the association of a partition with an image, is a difficult task. It can be decomposed in two steps: at first, a family of contours associated with a series of nested partitions (or hierarchy) is created and…
Accurate segmentation of breast lesions is a crucial step in evaluating the characteristics of tumors. However, this is a challenging task, since breast lesions have sophisticated shape, topological structure, and variation in the intensity…